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Relevance to Autism

Missense variants in the BPTF gene have been identified in ASD probands from the MSSNG cohort, the SPARK cohort, the Autism Sequencing Consortium, and most recently in a cohort of 75 Turkish patients diagnosed with ASD (Yuen et al., 2017; Zhou et al., 2022; Fu et al., 2022; Kayhan et al., 2026). De novo loss-of-function variants in this gene have been reported in ASD probands from the REACH cohort and a Spanish ASD cohort, as well as in an individual with autism from a ethnically diverse pediatric patient population (Ji et al., 2019; Antaki et al., 2022; Blzquez et al., 2025). ASD has also been reported in a subset of individuals with NEDDFL (2/10 in Stankiewicz et al., 2017, and 3/26 individuals in Glinton et al., 2021).

Molecular Function

This gene was identified by the reactivity of its encoded protein to a monoclonal antibody prepared against brain homogenates from patients with Alzheimer's disease. Analysis of the original protein (fetal Alz-50 reactive clone 1, or FAC1), identified as an 810 aa protein containing a DNA-binding domain and a zinc finger motif, suggested it might play a role in the regulation of transcription. High levels of FAC1 were detected in fetal brain and in patients with neurodegenerative diseases. The protein encoded by this gene is actually much larger than originally thought, and it also contains a C-terminal bromodomain characteristic of proteins that regulate transcription during proliferation. The encoded protein is highly similar to the largest subunit of the Drosophila NURF (nucleosome remodeling factor) complex. In Drosophila, the NURF complex, which catalyzes nucleosome sliding on DNA and interacts with sequence-specific transcription factors, is necessary for the chromatin remodeling

External Links

        

References

Type
Title
Type of Disorder
Associated Disorders
Author, Year
Primary
Genetic Traces in Autism Spectrum Disorders: A Whole Exome Sequencing Study from Türkiye
ASD
ADHD
Support
Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder
ASD
Support
Integrating de novo and inherited variants in 42
ASD
Support
A phenotypic spectrum of autism is attributable to the combined effects of rare variants, polygenic risk and sex
ASD
Support
Phenotypic expansion of the BPTF-related neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
Neurodevelopmental disorder with dysmorphic facies
ASD, ADHD
Support
Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism
ASD
Support
A semiautomated whole-exome sequencing workflow leads to increased diagnostic yield and identification of novel candidate variants
ASD, epilepsy/seizures
Support
Clinical and genetic findings in autism spectrum disorders analyzed using exome sequencing
ASD
ADHD, DD
Support
Haploinsufficiency of the Chromatin Remodeler BPTF Causes Syndromic Developmental and Speech Delay, Postnatal Microcephaly, and Dysmorphic Features
Neurodevelopmental disorder with dysmorphic facies
ASD
Support
Rare coding variation provides insight into the genetic architecture and phenotypic context of autism
ASD

Rare

Variant ID
Variant Type
Allele Change
Residue Change
Inheritance Pattern
Inheritance Association
Family Type
Author, Year
 GEN1539R001 
 missense_variant 
 c.4588C>G 
 p.Gln1530Glu 
 Unknown 
  
  
 GEN1539R002 
 missense_variant 
 c.402G>T 
 p.Glu134Asp 
 De novo 
  
 Simplex 
 GEN1539R003 
 synonymous_variant 
 c.6960A>G 
 p.Ser2320= 
 De novo 
  
  
 GEN1539R004 
 frameshift_variant 
 c.2203_2204del 
 p.Arg735fs 
 De novo 
  
  
 GEN1539R005 
 inframe_deletion 
 c.486_512del 
 p.Glu162_Asp170del 
 De novo 
  
 Multiplex 
 GEN1539R006 
 missense_variant 
 c.6364A>C 
 p.Thr2122Pro 
 De novo 
  
 Multiplex 
 GEN1539R007 
 splice_region_variant 
 c.5709-7C>T 
  
 De novo 
  
 Simplex 
 GEN1539R008 
 missense_variant 
 c.2168G>A 
 p.Arg723His 
 De novo 
  
  
 GEN1539R009 
 frameshift_variant 
 c.5715_5716delAG 
 p.Val1906GlufsTer15 
 De novo 
  
 Simplex 
 GEN1539R010 
 frameshift_variant 
 c.8562_8563del 
 p.Val2855SerfsTer7 
 De novo 
  
  
 GEN1539R011 
 frameshift_variant 
 c.2860dup 
 p.Glu954GlyfsTer5 
 De novo 
  
  
 GEN1539R012 
 frameshift_variant 
 c.5216_5217del 
 p.Val1739GlyfsTer96 
 Unknown 
 Not maternal 
  
 GEN1539R013 
 stop_gained 
 c.8650A>T 
 p.Lys2884Ter 
 De novo 
  
  
 GEN1539R014 
 copy_number_loss 
 c.-121653_2922-3575del 
  
 De novo 
  
  
 GEN1539R015 
 copy_number_loss 
 c.2922-1506_*8577del 
  
 Unknown 
  
  
 GEN1539R016 
 splice_site_variant 
 c.3360_3370+1del 
  
 De novo 
  
  
 GEN1539R017 
 missense_variant 
 c.5770G>A 
 p.Ala1924Thr 
 De novo 
  
  
 GEN1539R018 
 missense_variant 
 c.8558T>G 
 p.Met2853Arg 
 De novo 
  
  
 GEN1539R019 
 frameshift_variant 
 c.989del 
 p.Leu330ArgfsTer28 
 De novo 
  
  
 GEN1539R020 
 frameshift_variant 
 c.2744del 
 p.Asn915ThrfsTer36 
 De novo 
  
  
 GEN1539R021 
 frameshift_variant 
 c.209dupG 
 p.Ser71GlnfsTer3 
 Familial 
 Maternal 
  
 GEN1539R022 
 frameshift_variant 
 c.255delC 
 p.Ser86AlafsTer151 
 De novo 
  
 Simplex 
 GEN1539R023 
 frameshift_variant 
 c.255delC 
 p.Ser86AlafsTer151 
 De novo 
  
 Simplex 
 GEN1539R024 
 frameshift_variant 
 c.255dupC 
 p.Ser86GlnfsTer43 
 De novo 
  
 Simplex 
 GEN1539R025 
 stop_gained 
 c.1282G>T 
 p.Glu428Ter 
 De novo 
  
 Simplex 
 GEN1539R026 
 frameshift_variant 
 c.1607_1620del 
 p.Asp536GlyfsTer5 
 Unknown 
  
  
 GEN1539R027 
 frameshift_variant 
 c.2724_2727del 
 p.Thr909SerfsTer4 
 De novo 
  
 Simplex 
 GEN1539R028 
 splice_site_variant 
 c.2921+1G>C 
  
 Familial 
 Maternal 
  
 GEN1539R029 
 frameshift_variant 
 c.3085delA 
 p.Thr1029GlnfsTer27 
 De novo 
  
 Simplex 
 GEN1539R030 
 inframe_deletion 
 c.3210_3221del 
 p.Asn1071_Glu1074del 
 Familial 
 Paternal 
  
 GEN1539R031 
 frameshift_variant 
 c.3233_3237del 
 p.Arg1078MetfsTer13 
 Unknown 
  
  
 GEN1539R032 
 stop_gained 
 c.3610C>T 
 p.Arg1204Ter 
 Familial 
 Maternal 
  
 GEN1539R033 
 stop_gained 
 c.4555C>T 
 p.Arg1519Ter 
 De novo 
  
 Simplex 
 GEN1539R034 
 splice_site_variant 
 c.5936-1G>A 
 p.Thr1980GlufsTer25 
 De novo 
  
 Simplex 
 GEN1539R035 
 frameshift_variant 
 c.6078dup 
 p.Ala2027CysfsTer2 
 De novo 
  
 Simplex 
 GEN1539R036 
 splice_region_variant 
 c.6259+3_6259+4delinsG 
 p.? 
 De novo 
  
 Simplex 
 GEN1539R037 
 frameshift_variant 
 c.7521_7524dup 
 p.Leu2509IlefsTer21 
 De novo 
  
 Simplex 
 GEN1539R038 
 copy_number_loss 
 c.7875+3559_7876-2789del 
  
 De novo 
  
 Simplex 
 GEN1539R039 
 missense_variant 
 c.8081G>C 
 p.Arg2694Thr 
 Unknown 
  
  
 GEN1539R040 
 copy_number_loss 
 c.(7875+1_7876-1)_(8209+1_8210-1)del 
  
 De novo 
  
 Simplex 
 GEN1539R041 
 splice_region_variant 
 c.8210+6_8210+8del 
  
 De novo 
  
 Simplex 
 GEN1539R042 
 stop_gained 
 c.8278G>T 
 p.Glu2760Ter 
 De novo 
  
 Simplex 

Common

No Common Variants Available
Chromosome
CNV Locus
CNV Type
# of studies
Animal Model
17
Duplication
 1
 
17
Duplication
 1
 
17
Duplication
 1
 
17
Duplication
 1
 
17
Deletion
 2
 
17
Duplication
 1
 
17
Deletion
 1
 
17
Deletion
 13
 
17
Deletion
 2
 

No Animal Model Data Available

 

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